Detecting pairwise correlations in high-density recordings: open science in action
Stephen J Eglen
Acknowledgements
Ellese Cotterill, Catherine Cutts, Tom Edinburgh, Gerrit Hilgen, Evelyne Sernagor.
BBSRC, EPSRC, Wellcome Trust, Software Sustainibility Institute.
Correlating spike trains
Retinal waves: Wong et al (1993) (fig 8, 9)

How to interpret figures?
- three regions: [0,1], 1, [1, ∞]
- lower firing rates -> higher CI
What method should we use?
Phase 1: finding a short list
34 measures in literature + 1 from us => 35.
Six necessary properties:
- Symmetric
- Robust to variations in firing rate
- Robust to amount of data
- Bounded [-1, +1]
- Robust to variations in bin width (Δt)
- Anticorrelation: The measure should discriminate between no correlation and anticorrelation.
Dependence on firing rate
Phase 2: Desirable properties
Desirable properties:
- D1: Ignore periods when both neurons are inactive.
- D2: minimal assumptions on structure.
- D3: aside from Δt, minimise number of parameters
Four methods:
- Kerschensteiner and Wong correlation (D1, D2)
- Spike count correlation (D2, D3)
- Kruskal et al. binless correlation measure (D1?, D2, D3)
- Tiling coefficient (D1, D2, D3)
Tiling measure
Evidence
Blankenship et al (2011)
Correlations decay with age
Inference methods
Biorxiv paper.
Correlogram methods
Extending across time with tau.
Looking for needles in haystacks.
Desirable (binary) properties
of burst detectors
- Deterministic
- No assumptions on ISI distribution
- Minimal parameters
- Computational effeciency
Desirable (qualitative) properties
of burst detectors
- Non-bursting trains
- Non-stationary trains
- Regular short bursts
- Nonstationary bursts
- Regular long bursts
- High frequency bursts
- Noisy trains
Evaluation
Ranking of burst analysis methods
Burst analysis: mouse retinal neurons
Example trains of cells derived from human stem cells
Burst analysis:
networks derived from human stem cells
Open science and reproducible research
Reproducible research
To do this work we needed access to data. We have released this (Eglen et al 2014, Gigascience).
Then and now

Access to code
English is a poor way of unambigiously describing algorithms.
Claerbout and Donoho: the scholarship is not the article; the “scholarship is the complete software […]”
“Talk is cheap. Show me the code.” (Torvalds, 2000)
2/8 burst detectors were available (as R packages).